Basically, MBS doesn't want to air the final two episodes of Madoka for sensitivity reasons and doesn't care what SHAFT or Gen Urobuchi have to say about it.
We'll have to see how things turn out, though the worst case scenario is that the last two episodes aren't released until the DVDs come out around September.
(On second thought, I'm editing the URL out because I don't think it's right to involve that AnimeSuki guy in this. Most everyone knows the news by now anyway.)